From 60b3c92d17012e8cc034018c9b73a8140b76672a Mon Sep 17 00:00:00 2001 From: Thomas White Date: Thu, 7 Mar 2013 11:16:23 +0100 Subject: Add PartialityModel to docs --- doc/reference/libcrystfel/CrystFEL-sections.txt | 1 + 1 file changed, 1 insertion(+) (limited to 'doc') diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt index 720cabff..ff8001cf 100644 --- a/doc/reference/libcrystfel/CrystFEL-sections.txt +++ b/doc/reference/libcrystfel/CrystFEL-sections.txt @@ -380,6 +380,7 @@ crystal_set_user_flag
geometry +PartialityModel find_intersections select_intersections update_partialities -- cgit v1.2.3 From 2b115b938d8bfba13f4193e329728b09a750b79f Mon Sep 17 00:00:00 2001 From: Thomas White Date: Wed, 13 Mar 2013 10:43:42 +0100 Subject: Add Lorentz factor --- doc/reference/libcrystfel/CrystFEL-sections.txt | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'doc') diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt index ff8001cf..09267538 100644 --- a/doc/reference/libcrystfel/CrystFEL-sections.txt +++ b/doc/reference/libcrystfel/CrystFEL-sections.txt @@ -21,10 +21,11 @@ next_found_refl get_excitation_error get_detector_pos get_partiality +get_lorentz +get_partial get_indices get_symmetric_indices get_intensity -get_partial get_scalable get_refinable get_redundancy @@ -34,6 +35,8 @@ get_temp1 get_temp2 set_detector_pos +set_partiality +set_lorentz set_partial set_intensity set_scalable -- cgit v1.2.3 From 101aa5f9f8290b1d180d04d6ab5ff7eac934c148 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 15 Mar 2013 11:30:47 +0100 Subject: partial_sim: Add --osf-stddev --- doc/man/partial_sim.1 | 6 ++++++ 1 file changed, 6 insertions(+) (limited to 'doc') diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1 index 5b417978..9f3436ea 100644 --- a/doc/man/partial_sim.1 +++ b/doc/man/partial_sim.1 @@ -77,6 +77,12 @@ Add random values with a flat distribution to the components of the reciprocal l .PD Save a table of values to \fIfilename\fR containing, in resolution shells, the following columns: resolution shell centre in nm^-1, number of reflections in shell, mean partiality, maximum partiality. +.PD 0 +.B +.IP "\fB--osf-stddev=\fR\fIval\fR +.PD +Set the standard deviation of the distribution of overall scaling factors to \fIval\fR. The distribution will be cut at zero, i.e. negative or zero scaling factors are not allowed. The distribution will be centered on 1. The default is \fB--osf-stddev=2.0\fR. + .SH AUTHOR This page was written by Thomas White. -- cgit v1.2.3 From 9436a03fd02a464b1440f0b54cf9f3aaca5b2ded Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 15 Mar 2013 11:44:22 +0100 Subject: partial_sim: Add --full-stddev and --noise-stddev --- doc/man/partial_sim.1 | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) (limited to 'doc') diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1 index 9f3436ea..7321b9ff 100644 --- a/doc/man/partial_sim.1 +++ b/doc/man/partial_sim.1 @@ -1,7 +1,7 @@ .\" .\" partial_sim man page .\" -.\" Copyright © 2012 Thomas White +.\" Copyright © 2012-2013 Thomas White .\" .\" Part of CrystFEL - crystallography with a FEL .\" @@ -81,7 +81,19 @@ Save a table of values to \fIfilename\fR containing, in resolution shells, the f .B .IP "\fB--osf-stddev=\fR\fIval\fR .PD -Set the standard deviation of the distribution of overall scaling factors to \fIval\fR. The distribution will be cut at zero, i.e. negative or zero scaling factors are not allowed. The distribution will be centered on 1. The default is \fB--osf-stddev=2.0\fR. +Set the standard deviation of the distribution of overall scaling factors to \fIval\fR. The distribution will be cut at zero, i.e. negative or zero scaling factors are not allowed. The distribution will be Gaussian centered on 1. The default is \fB--osf-stddev=2.0\fR. + +.PD 0 +.B +.IP "\fB--full-stddev=\fR\fIval\fR +.PD +Set the standard deviation of the distribution of randomly generated full intensities to \fIval\fR. The distribution will be Gaussian, centered on zero, and the absolute value will be taken (i.e. there will be no negative values). The default is \fB--full-stddev=1000.0\fR. This option has no effect if you also use \fB-i\fR or \fR--input\fB. + +.PD 0 +.B +.IP "\fB--noise-stddev=\fR\fIval\fR +.PD +Set the standard deviation of the noise added to the partial intensities to \fIval\fR. The noise will be Gaussian, and the same for all reflections. The default is \fB--noise-stddev=20.0\fR. .SH AUTHOR This page was written by Thomas White. @@ -90,7 +102,7 @@ This page was written by Thomas White. Report bugs to , or visit . .SH COPYRIGHT AND DISCLAIMER -Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. +Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. .P partial_sim, and this manaul, are part of CrystFEL. .P -- cgit v1.2.3